Persistent infections with hepatitis C virus (HCV) are a major public health concern in the United States today. While diagnostic tests exist to identify and quantify HCV infections, there is a great need for analytical methods that provide detailed information about the molecular nature of HCV infections. HCV infections are marked by considerable genetic diversity, with at least six major genotypes of HCV. A readily available, rapid and accurate method to identify and quantitate infecting HCV genotype(s) would be valuable in guiding treatment, since it is well established that HCV genotype and viral load are predictive of response to interferon-based therapies. In addition, rapid and sensitive methods for early identification of drug-resistance mutations will be required to maximize the usefulness of new anti-HCV antiviral drugs now in clinical development. We propose to address these needs by developing HCV-specific applications for the T5000 Universal Biosensor, a novel diagnostics platform originally developed for biodefense applications that is currently being applied to human clinical diagnostics. By using mass spectrometry to analyze the products of PCR reactions, genotypes, mixed viral infections and drug resistance mutations can be identified and quantified from the same sample in a high-throughput and cost-effective fashion. The aims of this proposal are to: 1) Develop and validate a T5000-based assay for detection, quantitation, and genotype determination of HCV RNA present in the serum or plasma of infected individuals at =50 RNA IU/mL, and a quantitative dynamic range broader than 600-500,000 IU/ml that has the ability to identify the genotype of any viral RNA species contributing to =10% of the total. 2) Develop and validate T5000-based assays capable of detecting and typing mutations causing resistance to nucleoside analog inhibitors of the NS5B polymerase in addition to NS3/4A protease inhibitors. This proposal teams Ibis, the small business that developed the T5000 biosensor, with the NIAID-funded Hepatitis C Research Center at the University of Texas Medical Branch, Galveston. The expected products of this effort will be novel assay kits that address major unmet diagnostic needs of patients infected with HCV and that will assist Pharma in development of specific anti-viral therapies for HCV. The tests will be commercialized through reference laboratories or kits sold through partners in the commercial clinical diagnostics business. PUBLIC HEALTH RELEVANCE: Persistent infections with hepatitis C virus (HCV) are a major public health concern in the United States today. Approximately 4 million Americans are chronically infected with HCV and at risk for long-term complications including end-stage liver disease and liver cancer. We propose to develop diagnostic tests based upon new technology that can directly influence lifesaving medical decisions regarding optimal treatment of HCV infections and early detection of resistance to new antiviral drugs.